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To load gene expression data into the Brain Explorer viewer: go the Allen Mouse Brain Atlas and perform a gene search. You can type in a gene in the search box or click on a structure name to retrieve differential enriched genes. Your search brings back a list of experiments. Click on a row to select an experiment of interest. A 3D thumbnail of the expression pattern of that experiment will appear to the right. Click on the blue “3D” file link to launch the Brain Explorer application.

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When the Brain Explorer 3-D Viewer opens, you will be taken to a screen that displays the #Image Viewer, the #Structure Ontology Viewer, and the #Gene List.

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You can select a sphere by clicking on it. Spheres can be deselected by clicking on blank space. The original ISH image of the selected sphere will be displayed blended with the expression heat mask in the lower left hand portion of the screen. The blending can be adjusted by selecting Image Controls from the View menu and moving the Image Blending slider. Double-clicking on the zoomed ISH image will open the corresponding ISH image in a high resolution image viewer.

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The information at the upper left corner of the main Brain Explorer window summarizes the expression detected in the selected grid location. These numbers include the average expression density and intensity (over pixels). The Informatics Data Processing White Paper describes how the measurements were obtained.

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